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Halfdan Rydbeck
Profile
Recently developed a pipeline of rscripts to perform pathway and correlation network analysis of cord blood plasma proteomics data. Developed pipelines for automatic preprocessing and delivery of Illumina and Pacbio DNA sequencing output. Set up server infrastructure for NGS data handling. Manged NGS file servers, user access and data delivery. Examples of downstream analysis: Blasted an exon sequence against multiple assembled fish genomes to look for systematic loss in phylogeny. Analyzed bacterial methylomes, sequenced with Pacbio in, respect to virulens. PhD project. Developed an R package for clustering of genomic tracks. Scripts developed in R and The Genomic Hyperbrowser was used to study the dependencies and select genes, based on genomic, epigenomic and transcriptomic alterations in samples from osteosarcoma and immune cells. The gene expression, promoter methylation and DNA copy number data were acquired by oligonucleotide microarray technology, and the histone modification data was acquired by technology based on chromatin immune precipitation and next generation sequencing, ChIP-seq.
Research Experience
Researacher bioinformatics
Core Facilities Bioinformatics vid Sahlgrenska Akademin, Univeristy of Gothenburg
Göteborg, Sweden
2022 - 2020
- Worked with Rstudio and the R package collections Bioconductor and Tidyverse. Reports where generated with R notebooks and the R package Bookdown. Github and GitKraken is used for code version control. Recently applied R packages are DEqMS for differential expression analysis of mass spectrometry data, WGCNA for proteins correlation analysis and ReactomeGSA for pathway analysis
Senior engineer bioinformatics
Norwegian Sequencing Center
University of Oslo, Norway
2017 - 2014
- System setup, user management, data preprocessing, delivery and down stream analysis of Illumina and Pacbio sequence data at the Norwegian DNA sequencing center. Work
Principal engineer
Bioinformatics core facility
Rikshospitalet HF, Norway
2008 - 2007
- Microarray gene expression analysis
- Developing network-based methods to investigate and visualize clinically relevant patterns in data.
Research assistant
Human Genetics division
Children’s Hospital of Philadelphia, USA
2007 - 2006
- Bash and scripting for data wrangling and testing Solar, Plink, TDT, Merlin, STATA, SAS, R
- Work primarily done in R Shiny and Javascript (node and d3js).
Senior research assistant
Dept. of genetic epidemiology
A. I duPont Hospital for Children, USA
2005 - 2004
- Used software for genetic linkage and association studies of diseases/syndroms Velocardiofacial Syndrome, ADHD, Neuroblastoma, Osteoporosis, Cornelia de Lange’s syndrome and Myopia • Solar, Plink, TDT, Merlin, STATA, SAS, R
Database coordinator
Human Genetics division
Children’s Hospital of Philadelphia, USA
2004 - 2002
- Manged a database for SNP information Progeny2000
Teaching Experience
I like when teaching and learning is relaxing and joyfull
R for reprodicible scientific programming
Software carpentry
Oslo Norway
2018 - 2017
- Covered introduction to R language for statistics applications
- Graduate level class
Version controlling with git and github
Software carpentry
Oslo Norway
2018 - 2017
- Topics covered from penalized regression to boosted trees and neural networks
- Highest level course offered in department
Unix
Software carpentry
Oslo Norway
2018 - 2017
- Covered modern statistical computing algorithms
- 4th year PhD level class
Education
Sometimes I am almost tireless. This means that I fight hard so that the tasks or projects I undertake are completed on time and I do not give up until I’ve achieved the intended result
PhD bioinformatics
Medical faculty, University of Oslo
Oslo, Norway
2012 - 2007
- • Thesis title: Integrative epigenome analysis • courses mostly statistics (30p) • Analysed gene expression, promoter methylation, histone occupancy and copynumber variation data with R and The Genomic Hyperbrwser. Developed and R package for clustering of genomic tracks.
- University Graduate Fellow
Master of Science in Bioinformatics
Chalmers University of Technology
Gothenburg, Sweden
2001 - 2000
Master of Science in Molecular biology
University of Gothenburg /Uppsala
Göteborg/Uppsala, Sweden
1999 - 1993
Selected Publications, Posters, and Talks
References are availabel upon request
The proteome signature of cord blood plasma with high hematopoietic stem and progenitor cell count
Stem Cell Research
N/A
2022 - 2022
- Authored with Anders K.Nilsson, Annika Thorsell, Sofia Frändberg,Helena Barreto Henriksson, Camilla Hesse, Gunnel Hellgren, Pia Lundgren, AnnHellström